Recent inspections of abortion clinics by the Care Quality Commission could be used by politically motivated groups and “recruited into an orchestrated approach to restrict abortion”, the Royal College of Obstetricians and Gynaecologists has privately warned the NHS’s medical director.

The Guardian has seen strongly worded correspondence to Professor Sir Bruce Keogh from RCOG, in which the college expresses a range of concerns about the impact of the unannounced inspection of more than 250 clinics in England at the end of March on the orders of the health secretary, Andrew Lansley.

“The CQC investigations, unless carefully and sensitively handled, could have the potential to be used by politically motivated groups and individuals and be recruited into an orchestrated approach to restrict abortion,” says the letter from the college’s president, Dr Tony Falconer, and Dr Christopher Wilkinson, president of its faculty of sexual and reproductive healthcare.

It adds: “Separate to the CQC investigations, the high-profile campaign against abortion services may act as a further deterrent against women who become very frightened and fail to present at a time when they need access to these services.”

The CQC has been considering what regulatory action it will be taking following the inspections and is expected publish individual reports very soon.

The RCOG letter, marked “private and confidential”, was sent on 27 April to Keogh after a meeting with him was postponed.

It starts: “I write to you on a matter of some urgency about possible risks to the provision of abortion services to women within England resulting from the recent CQC inspections. We hope that you will be able to influence any responses in this sensitive and difficult area to reduce any risks to the maintenance of these services.”

Doctors working in abortion care now feel “very isolated and vulnerable”, they say. “Their general perception is that they have been unfairly targeted by the Department of Health.

Noting that the CQC investigations resulted in the suspension of some doctors by their hospital trusts, Falconer and Wilkinson add: “This has also led to reactive and thus clumsy bureaucracy being imposed by management, fearful that their processes may come under further scrutiny. The threat of criminal prosecution has understandably lowered morale amongst the already small pool of doctors providing the service.

“It would not be surprising if the effect of current actions is to deter junior doctors from training in the field and our current advanced training skills module in abortion care attracts very few training doctors, which does not bode well for the future.”

A Department of Health spokesperson said: “Our first priority has to be to protect women at what can be a very traumatic time. It is essential that they get proper advice and medical attention before deciding to have an abortion.”

“The Care Quality Commission presented us with very serious allegations that the law may have been broken, which is why we asked them to investigate this further. The CQC carries out unannounced inspections on a range of healthcare providers such as hospitals, care homes and dentists every day.

“Abortion clinics have not been singled out – if the government is presented with evidence that the law may be being broken, we have a duty to act on that.”

He added that the public health minister, Anne Milton, and Keogh had both subsequently met with RCOG. “They agreed that we would work with RCOG to ensure that women receive a safe, legal abortion service.”